考研-生化分子生物学

关键术语

Thegenome(基因组)isthecompletesetofgenesofanorganism.UltimatelyitisdefinedbythecompleteDNAsequence,althoughasapracticalmatteritmaynotbepossibletoidentifyeverygeneunequivocallysolelyonthebasisofsequence.

Thetranscriptome(转录物组)

isthecompletesetofgenesexpressedunderparticularconditions.ItisdefinedintermsofthesetofmRNAmoleculesthatispresent,andcanrefertoasinglecelltypeortoanymorecomplexassemblyofcellsuptothecompleteorganism.

Theproteome

(蛋白质组)

isthecompletesetofproteins.Itshouldcorrespondtothetranscriptome,althoughtherecanbedifferencesofdetailreflectingchangesintherelativeabundanceorstabilitiesofmRNAsandproteins.

第3章基因的数目C-value

(C值)isthequantityofDNAinthegenome(perhaploidsetofchromosomes).ThereisenormousvariationintherangeofC-values,from<106bpforamycoplasma(支原体)to>1011bpforsomeplantsandamphibians.

NonrepetitiveDNA(非重复序列DNA)showsreassociationkineticsexpectedofuniquesequences.

RepetitiveDNA

(重复序列DNA)behavesinareassociationreactionasthoughmany(relatedoridentical)sequencesarepresentinacomponent,allowinganypairofcomplementarysequencestoreassociate.第3章基因的数目第1节为什么基因组如此之大?关键术语第3章基因的数目第1节为什么基因组如此之大?

低等真核生物的单倍体DNA含量与形态学的复杂性相关，而在高等真核生物中，变化很大。下图为不同生物门类DNA含量的分布。有花植物鸟类哺乳类爬行类两栖类有骨鱼类软骨鱼类棘皮类甲壳类昆虫软体动物蠕虫霉菌藻类真菌革兰氏阳性细菌革兰氏阴性细菌支原体蟾蜍和人类具有同样的最小量基因组DNA.但是我们认为人类的遗传复杂性显然要大于蟾蜍.有些种系不同种生物之间的基因组DNA量差异极大而复杂性却没有大的不同,尤其是昆虫、两栖类和植物（可大于2个数量级），但鸟类和爬行类生物种间则基因组DNA量差异不大。第3章基因的数目第1节为什么基因组如此之大?一般来说，不同种系生物基因组大小的最底限度从原核生物至哺乳类随复杂性增加而增加.基因组所占的DNA远远大于编码蛋白质所需;某些复杂程度相仿的同类生物（如两栖类），其基因组相差可达100倍（非编码DNA序列）。第3章基因的数目第1节为什么基因组如此之大?TheC-valueparadoxreferstothelackofacorrelationbetweengenomesizeandgeneticcomplexity.

Itisnotpossibletodeducefromtheoverallsizeofthegenomeanythingaboutthenumberofgenes.问题：基因组越大，是否所含的基因总数越多？二层意思：1.独特基因增多；2.某些基因的拷贝数增加。解决：1.最终依赖DNA测序；

2.真核基因组一般特性可通过变性DNA复性动力学进行评估。

变性DNA复性动力学可以将DNA分为

非重复序列DNA和重复序列DNA二类非重复序列DNA：序列独特，半合子中只有一个拷贝重复序列DNA：不参与编码蛋白质。

中度重复序列DNA：序列较短，10-1000个拷贝，遍布基因组，与RNA前体高级结构形成有关。高度重复序列DNA：序列很短（常<100bp），数千拷贝以上，常成串排列。第3章基因的数目第1节为什么基因组如此之大?真核基因组不同序列组分的比例。非重复序列DNA的绝对含量随基因组增大而增加，但2x109bp是个平台.

看来，非重复序列DNA的绝对含量与生物的复杂性似乎一致性更好。第3章基因的数目第1节为什么基因组如此之大?基因组序列的全长测序使我们弄清了几种生物的基因组大小和基因数目(Arabidopsis,Drosophila,andmanareestimatedfrompartialdata).致死基因座的数目是通过遗传学数据估测而来。

线虫v果蝇第3章基因的数目第2节一些生物的基因总数在果蝇,约20%的基因编码与基因表达和维持的蛋白,约20%编码酶蛋白,<10%编码与细胞周期或信号转导的蛋白,其他半数基因编码功能未知的蛋白。

第3章基因的数目第2节一些生物的基因总数由于许多基因是由祖先基因复制和进化而来的，所以基因家族的数目远少于基因的总数。

第3章基因的数目第2节一些生物的基因总数Proteinsizeincreasesfromprokaryotestoeukaryotes.theaveragevertebratecellexpresses~10,00020,000genes.Eukaryoticgenesaretranscribedindividually,eachgeneproducingamonocistronicmessenger.Whatisthecoreproteomethebasicnumberofthedifferenttypesofproteinsintheorganism?Aminimumestimateisgivenbythenumberofgenefamilies,rangingfrom1400inthebacterium,>4000intheyeast,and9500and8000inthewormandfly,respectively.第3章基因的数目第2节一些生物的基因总数果蝇基因组包括编码真核生物共有的基因、多细胞真核基因共有的基因和亚群生物（包括果蝇）更为特异的基因。第3章基因的数目第2节一些生物的基因总数Naturalselectionistheforcethatensuresthatusefulgenesareretainedinthegenome.

Themaintenanceofageneimpliesthatitconfersaselectiveadvantageontheorganism.

Oneapproachtotheissueofgenenumberistodeterminethenumberofessentialgenesbymutationalanalysis.

Anymutationthatislethalistakentoidentifyalocusthatisessentialfortheorganism.

（mutationlethalgenesessentialgenes)第3章基因的数目第3节有多少必须基因？Mycoplasmagenitalium,2/3,andE.coli<50%appeartobeessential.YeastS.cerevisiae12%arelethal,andanother14%impededgrowth.Questions:Keyquestionsthatremaintobeansweredsystematicallyare:Whatproportionofthetotalnumberofgenesisessential,inhowmanydomutationsproduceatleastdetectableeffects,andaretheregenesthataregenuinelydispensable?Subsidiaryquestionsaboutthegenomeasawholeare:Whatarethefunctions(ifany)ofDNAthatdoesnotresideingenes?Whateffectdoesalargechangeintotalsizehaveontheoperationofthegenome,asinthecaseoftherelatedamphibians?第3章基因的数目第3节有多少必须基因？第4章基因的成簇和重复

关键术语Genefamily:asetofgenesdescendedbyduplicationandvariationfromsomeancestralgene.Geneclusters:rangefromextremeswhereaduplicationhasgeneratedtwoadjacentrelatedgenestocaseswherehundredsofidenticalgeneslieinatandemarray(e.g.rRNAandhistonegenes)Satellite,Minisatellite,MicrosatelliteDNA:thehighlyrepetitivefractionofthegenomeconsistsofmultipletandemcopiesofveryshortrepeatingunit(inertregionsofchromosomes,centromeres).(100kb~Mb,0.1kb~20kb,<150bp)Pseudogenes:nonfunctionalgeneswhichareunabletocodeforproteins(deficienciesintranscription/translation).第4章基因的成簇和重复

Tandemduplicationmayarisethrougherrorsinreplicationorbination(Exonorwholegene).Separation(divergence)ofduplicatescanoccurbyachromosmaltranslocation.

形成的机理第4章基因的成簇和重复第一节基因簇是由复制和分散形成的

Eachofthe-likeand-likeglobingenefamiliesisorganizedintoasingleclusterthatincludesfunctionalgenesandpseudogenes().Theorganizationoftheclustersinhigherprimatesisconserved.Theactivegenesaretranscribedfromlefttoright.第4章基因的成簇和重复第一节基因簇是由复制和分散形成的

Allglobingeneshaveevolvedbyaseriesofduplications,transpositions,andmutationsfromasingleancestralgene(豆血红蛋白).800millionyearsago500millionyearsago350millionyearsago第4章基因的成簇和重复第二节rRNA基因构成串联重复单位

Inbacteria,themultiplerRNAgenepairsaredispersed.Inmosteukaryoticnuclei,therRNAgenesarecontainedinatandemclusterorclusters.Atandemgeneclusterhasanalternationoftranscriptionunitandnontranscribedspacerandgeneratesacircularrestrictionmap.

第4章基因的成簇和重复第一节基因簇是由复制和分散形成的

第4章基因的成簇和重复第二节rRNA基因构成串联重复单位

Inbacteria,themultiplerRNAgenepairsaredispersed.Inmosteukaryoticnuclei,therRNAgenesarecontainedinatandemclusterorclusters.TranscriptionofrDNAclustersgeneratesaseriesofmatrices,eachcorrespondingtoonetranscriptionunitandseparatedfromthenextbythenontranscribedspacer.第4章基因的成簇和重复第二节rRNA基因构成串联重复单位

SummaryAlmostallgenesbelongtofamilies.Familiesevolvebytheduplicationofagene(orgenes),followedbydivergencebetweenthecopies.Somecopiessufferinactivatingmutationsandepseudogenesthatnolongerhaveanyfunction.Anevolvingsetofgenesmayremaintogetherinaclusterormaybedispersedtonewlocationsbychromosomalrearrangement.Atandemclusterconsistsofmanycopiesofarepeatingunitthatincludesthetranscribedsequence(s)andanontranscribedspacer(s).

SatelliteDNAconsistsofveryshortsequencesrepeatedmanytimesintandem.SatelliteDNAisconcentratedincentromericheterochromatin,butitsfunction(ifany)isunknown.Minisatelliteshavepropertiessimilartosatellites,butaremuchsmaller;theyareusefulforhumangenomicmapping.

第19章核小体

Thenucleosomeisthesubunitofallchromatin

ThenucleosomeconsistsofapproximatelyequalmassesofDNAandhistones(includingH1).Thepredictedmassofthenucleosomeis262kD.

Thenucleosomecontains~200bpofDNAassociatedwithahistoneoctamerthatconsistsoftwocopieseachofH2A,H2B,H3,andH4.Theseareknownasthecorehistones.第19章核小体

Theshapeofthenucleosomecorrespondstoaflatdiskorcylinder,ofdiameter11nmandheight6nm.ThelengthoftheDNAisroughlytwicethe~34nmcircumferenceoftheparticle（180~200bp）.第19章核小体

第19章核小体MicrococcalnucleasedigestschromatininnucleiintoamultimericseriesofDNAbandsthatcanbeseparatedbygelelectrophoresis.第19章核小体

DNAiscoiledinarraysofnucleosomesCoreDNAisthe146bpofDNAcontainedonacoreparticle.

Coreparticleisadigestionproductofthenucleosomethatretainsthehistoneoctamerandhas146bpofDNA;itsstructureappearssimilartothatofthenucleosomeitself.第19章核小体

Micrococcalnucleasereducesthelengthofnucleosomemonomersindiscretesteps.

第19章核小体第19章核小体

The10nmfiberisacontinuousstringofnucleosomes

The30nmfibermayhaveahelicalcoilof6nucleosomesperturn,organizedradially.第19章核小体Themostlikelyarrangementforpackingnucleosomesintothefiberisasolenoid（螺线管）,illustratedinFigure.Thenucleosomesturninahelicalarray,withanangleof~600betweenthefacesofadjacentnucleosomes第19章核小体

Organizationofthehistoneoctamer

Inasymmetricalmodelforthenucleosome,theH32-H42tetramerprovidesakernelfortheshape.OneH2A-H2Bdimercanbeseeninthetopview;theotherisunderneath.

第19章核小体

Aretranscribedgenesorganizedinnucleosomes?RNApolymeraseiscomparableinsizetothenucleosomeandmightencounterdifficultiesinfollowingtheDNAaroundthehistoneoctamer.

第19章核小体

FigureshowswhathappenswhenanRNApolymerasetranscribesashortpieceofDNAcontainingasingleoctamercoreinvitro.ThecoreremainsassociatedwiththeDNA,butisfoundinadifferentlocation.第19章核小体

第19章核小体

AnucleosomecontainsacharacteristiclengthofDNA,usually~200bp,wrappedaroundanoctamercontainingtwocopieseachofhistonesH2A,H2B,H3,andH4.AsingleH1proteinisassociatedwitheachnucleosome.Nucleosomesareorganizedintoafiberof30nmdiameterwhichhas6nucleosomesperturnandapackingratioof40.RemovalofH1allowsthisfibertounfoldintoa10nmfiberthatconsistsofalinearstringofnucleosomes.The30nmfiberprobablyconsistsofthe10nmfiberwoundintoasolenoid.The30nmfiberisthebasicconstituentofbotheuchromatinandheterochromatin;Nonhistoneproteinsareresponsibleforfurtherorganizationofthefiberintochromatinorchromosomeultrastructure.

SUMMARY

核心概念Chromatin(染色质)describestheconditionofthechromosomalmaterialduringtheinterphase(betweenmitoses)ofthecellcycle.

Chromosome

(染色体)isadiscreteunitofthegenomecarryingmanygenes.Eac